Jernej Zidar wrote:
Hi Mark.
How will pdb2gmx "know" it has to parse the monomeres.rtp file?
It can't. You must add to an existing .rtp file.
That's a problem (and a negative surprise), because I can't just add a
new residue to the aminoacids.rtp in Charmm27.ff folder. Charmm27 and
CGenFF are two different things, though they can be used together.
The CGenFF files can be found on the Gromacs website:
http://www.gromacs.org/Downloads/User_contributions/Force_fields
To make them fully functional and capable of using pdb2gmx, you would have to
add several files - .rtp, .hdb, .atp, and probably a few others.
I will add that you will also have to add the residue to aminoacids.dat
file, so that the polymer repeat unit is recognized. for your small
polymer molecule you can just generate from the swissparam website
That could well work in the case of the smallest polymer that is
composed of just five monomers, but it is absolutely out of the
question in the case of experimentally-relevant polymers that are
composed of at least 40 units.
How many different monomers are involved? Repeat units and polymeric assemblies
are precisely what pdb2gmx is for (consider the trivial example of a protein).
For further polymer-related tips, see the following:
http://www.gromacs.org/Documentation/How-tos/Polymers
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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